Server 2003 R2 was a relatively minor update and in many ways. The kernel didn't change, it only added certain features, SOME of which were freely available to download. (To be clear, some of the features added WERE significant (DFSR for example), but in my opinion, an OS upgrade - which 2003 R2 was called - should involve a kernel update. (It was released as an upgrade as opposed to a free update in part because microsoft wanted to make those who purchased software assurance feel they were getting their money's worth*)
Server 2008 R2 IS a kernel change as it's based on Windows 7's kernel and includes many enhancements in a variety of areas. It has been dubbed R2 to signify that the CALs you purchased for 2008 will remain valid with 2008 R2 DESPITE the kernel change.
Especially if you are upgrading a VM based 2008 server, I would strongly recommend creating a backup of the VM Hard Drive before hand (I'd recommend that regardless whenever you make a major OS change).
*Or so I've heard